• 13759 Citations
20072020

Research output per year

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Personal profile

Research Interests

I was one of the first students to obtain an undergraduate degree in Bioinformatics and Computational Biology at University of Toronto. Then, I trained as a computational biologist at Duke University (PhD) under Drs. Greg Crawford and Terry Furey focusing on gene regulation, specifically, using high-throughput sequencing assays to study chromatin dynamics across diverse human cell lines. For my postdoc, I joined Ido Amit's lab in Immunogenomics at the Weizmann Institute of Science in Israel where I applied genomic approaches to the study of immunology. My landmark paper showed that tissue-resident macrophages are capable of adopting tissue-specific functions by reprogramming their chromatin landscape in response to signal from the local environment.

As a computational immunologist, I interested in mapping the gene regulatory networks of immune cells in health and disease, particularly macrophages in rheumatic disease. As a plastic immune cell type, macrophages are found throughout the body where they play an important role in both homeostatic functions and immune response. The are critical to the pathogenesis of autoimmune diseases, such as rheumatoid arthritis and systemic sclerosis. Using high-throughput sequencing assays and computational techniques, I seek to profile the transcriptional and epigenomic profile of macrophages in different tissues in mouse models and patients with these diseases. We believe that a better understanding of the function and malfunction of macrophages we enable to develop more precise and effective treatments.

Education/Academic qualification

PhD, Duke University

… → 2013

Research interests

  • Arthritis - Rheumatoid
  • Big Data
  • Bioinformatics
  • Chromatin
  • Computational Biology
  • Epigenetics
  • Gene Regulation
  • Genomics
  • Immunology
  • Rheumatology
  • Scleroderma
  • Systems Biology

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Grants

  • Research Output

    • 13759 Citations
    • 26 Article
    • 4 Review article
    • 2 Short survey
    • 1 Comment/debate

    A Novel Microglia-Specific Transcriptional Signature Correlates With Behavioral Deficits in Neuropsychiatric Lupus

    Makinde, H. M., Winter, D. R., Procissi, D., Mike, E. V., Stock, A. D., Kando, M. J., Gadhvi, G. T., Droho, S., Bloomfield, C. L., Dominguez, S. T., Mayr, M. G., Lavine, J. A., Putterman, C. & Cuda, C. M., Feb 26 2020, In : Frontiers in immunology. 11, 230.

    Research output: Contribution to journalArticle

    Open Access
  • Microglia Adopt Longitudinal Transcriptional Changes After Traumatic Brain Injury

    Makinde, H. M., Just, T. B., Gadhvi, G. T., Winter, D. R. & Schwulst, S. J., Feb 1 2020, In : Journal of Surgical Research. 246, p. 113-122 10 p.

    Research output: Contribution to journalArticle

  • 1 Scopus citations

    Lipocalin-2 is a pathogenic determinant and biomarker of neuropsychiatric lupus

    Mike, E. V., Makinde, H. M., Gulinello, M., Vanarsa, K., Herlitz, L., Gadhvi, G., Winter, D. R., Mohan, C., Hanly, J. G., Mok, C. C., Cuda, C. M. & Putterman, C., Jan 2019, In : Journal of Autoimmunity. 96, p. 59-73 15 p.

    Research output: Contribution to journalArticle

  • 10 Scopus citations

    Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis

    Reyfman, P. A., Walter, J. M., Joshi, N., Anekalla, K. R., McQuattie-Pimentel, A. C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C. I., Ren, Z., Verma, R., Abdala-Valencia, H., Nam, K., Chi, M., Han, S. H., Gonzalez-Gonzalez, F. J., Soberanes, S., Watanabe, S., Williams, K. J. N., Flozak, A. S. & 29 others, Nicholson, T. T., Morgan, V. K., Winter, D. R., Hinchcliff, M., Hrusch, C. L., Guzy, R. D., Bonham, C. A., Sperling, A. I., Bag, R., Hamanaka, R. B., Mutlu, G. M., Yeldandi, A. V., Marshall, S. A., Shilatifard, A., Amaral, L. A. N., Perlman, H. R., Sznajder, J. I., Christine Argento, A., Gillespie, C. T., Dematte, J., Jain, M., Singer, B., Ridge, K. M., Lam, A. P., Bharat, A., Bhorade, S. M., Gottardi, C., Budinger, GR. S. & Misharin, A., Jun 15 2019, In : American Journal of Respiratory and Critical Care Medicine. 199, 12, p. 1517-1536 20 p.

    Research output: Contribution to journalArticle

    Open Access
  • 78 Scopus citations

    A beginner’s guide to analysis of RNA sequencing data

    Koch, C. M., Chiu, S. F., Akbarpour, M., Bharat, A., Ridge, K. M., Bartom, E. T. & Winter, D. R., Aug 2018, In : American journal of respiratory cell and molecular biology. 59, 2, p. 145-157 13 p.

    Research output: Contribution to journalReview article

  • 7 Scopus citations